D’or: deep orienter of protein–protein interaction networks

Motivation: Protein–protein interactions (PPIs) provide the skeleton for signal transduction in the cell. Current PPI measurement techniques do not provide information on their directionality which is critical for elucidating signaling pathways. To date, there are hundreds of thousands of known PPIs in public databases, yet only a small fraction of them have an assigned direction. This information gap calls for computational approaches for inferring the directionality of PPIs, aka network orientation. Results: In this work, we propose a novel deep learning approach for PPI network orientation. Our method first generates a set of proximity scores between a protein interaction and sets of cause and effect proteins using a network propagation procedure. Each of these score sets is fed, one at a time, to a deep set encoder whose outputs are used as features for predicting the interaction’s orientation. On a comprehensive dataset of oriented PPIs taken from five different sources, we achieve an area under the precision–recall curve of 0.89–0.92, outperforming previous methods. We further demonstrate the utility of the oriented network in prioritizing cancer driver genes and disease genes.